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Shaw C, Weimer BC, Gann R, Desai PT, Shah JD. The Yin and Yang of pathogens and probiotics: interplay between Salmonella enterica sv. Typhimurium and Bifidobacterium infantis during co-infection. Front Microbiol 2024; 15:1387498. [PMID: 38812689 PMCID: PMC11133690 DOI: 10.3389/fmicb.2024.1387498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 04/12/2024] [Indexed: 05/31/2024] Open
Abstract
Probiotic bacteria have been proposed as an alternative to antibiotics for the control of antimicrobial resistant enteric pathogens. The mechanistic details of this approach remain unclear, in part because pathogen reduction appears to be both strain and ecology dependent. Here we tested the ability of five probiotic strains, including some from common probiotic genera Lactobacillus and Bifidobacterium, to reduce binding of Salmonella enterica sv. Typhimurium to epithelial cells in vitro. Bifidobacterium longum subsp. infantis emerged as a promising strain; however, S. Typhimurium infection outcome in epithelial cells was dependent on inoculation order, with B. infantis unable to rescue host cells from preceding or concurrent infection. We further investigated the complex mechanisms underlying this interaction between B. infantis, S. Typhimurium, and epithelial cells using a multi-omics approach that included gene expression and altered metabolism via metabolomics. Incubation with B. infantis repressed apoptotic pathways and induced anti-inflammatory cascades in epithelial cells. In contrast, co-incubation with B. infantis increased in S. Typhimurium the expression of virulence factors, induced anaerobic metabolism, and repressed components of arginine metabolism as well as altering the metabolic profile. Concurrent application of the probiotic and pathogen notably generated metabolic profiles more similar to that of the probiotic alone than to the pathogen, indicating a central role for metabolism in modulating probiotic-pathogen-host interactions. Together these data imply crosstalk via small molecules between the epithelial cells, pathogen and probiotic that consistently demonstrated unique molecular mechanisms specific probiotic/pathogen the individual associations.
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Affiliation(s)
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, 100K Pathogen Genome Project, University of California, Davis, Davis, CA, United States
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2
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Yang WH, Aziz PV, Heithoff DM, Kim Y, Ko JY, Cho JW, Mahan MJ, Sperandio M, Marth JD. Innate mechanism of mucosal barrier erosion in the pathogenesis of acquired colitis. iScience 2023; 26:107883. [PMID: 37752945 PMCID: PMC10518488 DOI: 10.1016/j.isci.2023.107883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 08/16/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
The colonic mucosal barrier protects against infection, inflammation, and tissue ulceration. Composed primarily of Mucin-2, proteolytic erosion of this barrier is an invariant feature of colitis; however, the molecular mechanisms are not well understood. We have applied a recurrent food poisoning model of acquired inflammatory bowel disease using Salmonella enterica Typhimurium to investigate mucosal barrier erosion. Our findings reveal an innate Toll-like receptor 4-dependent mechanism activated by previous infection that induces Neu3 neuraminidase among colonic epithelial cells concurrent with increased Cathepsin-G protease secretion by Paneth cells. These anatomically separated host responses merge with the desialylation of nascent colonic Mucin-2 by Neu3 rendering the mucosal barrier susceptible to increased proteolytic breakdown by Cathepsin-G. Depletion of Cathepsin-G or Neu3 function using pharmacological inhibitors or genetic-null alleles protected against Mucin-2 proteolysis and barrier erosion and reduced the frequency and severity of colitis, revealing approaches to preserve and potentially restore the mucosal barrier.
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Affiliation(s)
- Won Ho Yang
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Diseases Center; La Jolla, CA 92037, USA
- Glycosylation Network Research Center and Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Peter V. Aziz
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Diseases Center; La Jolla, CA 92037, USA
| | - Douglas M. Heithoff
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Yeolhoe Kim
- Glycosylation Network Research Center and Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jeong Yeon Ko
- Glycosylation Network Research Center and Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jin Won Cho
- Glycosylation Network Research Center and Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Michael J. Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Markus Sperandio
- Walter Brendel Center for Experimental Medicine, Institute of Cardiovascular Physiology and Pathophysiology, Ludwig Maximilians University, Munich, Germany
| | - Jamey D. Marth
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Diseases Center; La Jolla, CA 92037, USA
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3
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Heithoff DM, Barnes V L, Mahan SP, Fried JC, Fitzgibbons LN, House JK, Mahan MJ. Re-evaluation of FDA-approved antibiotics with increased diagnostic accuracy for assessment of antimicrobial resistance. Cell Rep Med 2023; 4:101023. [PMID: 37116500 PMCID: PMC10213814 DOI: 10.1016/j.xcrm.2023.101023] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/16/2023] [Accepted: 04/05/2023] [Indexed: 04/30/2023]
Abstract
Accurate assessment of antibiotic susceptibility is critical for treatment of antimicrobial resistant (AMR) infections. Here, we examine whether antimicrobial susceptibility testing in media more physiologically representative of in vivo conditions improves prediction of clinical outcome relative to standard bacteriologic medium. This analysis reveals that ∼15% of minimum inhibitory concentration (MIC) values obtained in physiologic media predicted a change in susceptibility that crossed a clinical breakpoint used to categorize patient isolates as susceptible or resistant. The activities of antibiotics having discrepant results in different media were evaluated in murine sepsis models. Testing in cell culture medium improves the accuracy by which MIC assays predict in vivo efficacy. This analysis identifies several antibiotics for treatment of AMR infections that standard testing failed to identify and those that are ineffective despite indicated use by standard testing. Methods with increased diagnostic accuracy mitigate the AMR crisis via utilizing existing agents and optimizing drug discovery.
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Affiliation(s)
- Douglas M Heithoff
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Lucien Barnes V
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Scott P Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Jeffrey C Fried
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, CA 93105, USA; Department of Pulmonary and Critical Care Medicine, Santa Barbara Cottage Hospital, Santa Barbara, CA 93105, USA
| | - Lynn N Fitzgibbons
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, CA 93105, USA; Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, CA 93105, USA
| | - John K House
- Faculty of Science, School of Veterinary Science, The University of Sydney, Camden, NSW 2570, Australia.
| | - Michael J Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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4
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Heindel D, Chen S, Aziz PV, Chung JY, Marth JD, Mahal LK. Glycomic Analysis Reveals a Conserved Response to Bacterial Sepsis Induced by Different Bacterial Pathogens. ACS Infect Dis 2022; 8:1075-1085. [PMID: 35486714 PMCID: PMC9112329 DOI: 10.1021/acsinfecdis.2c00082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Indexed: 12/15/2022]
Abstract
Sepsis is an extreme inflammatory response to infection that occurs in the bloodstream and causes damage throughout the body. Glycosylation is known to play a role in immunity and inflammation, but the role of glycans in sepsis is not well-defined. Herein, we profiled the serum glycomes of experimental mouse sepsis models to identify changes induced by 4 different clinical bacterial pathogens (Gram-positive: Streptococcus pneumoniae and Staphylococcus aureus, Gram-negative: Escherichia coli and Salmonella Typhimurium) using our lectin microarray technology. We observed global shifts in the blood sera glycome that were conserved across all four species, regardless of whether they were Gram positive or negative. Bisecting GlcNAc was decreased upon sepsis and a strong increase in core 1/3 O-glycans was observed. Lectin blot analysis revealed a high molecular weight protein induced in sepsis by all four bacteria as the major cause of the core 1/3 O-glycan shift. Analysis of this band by mass spectrometry identified interalpha-trypsin inhibitor heavy chains (ITIHs) and fibronectin, both of which are associated with human sepsis. Shifts in the glycosylation of these proteins were observed. Overall, our work points toward a common mechanism for bacterially induced sepsis, marked by conserved changes in the glycome.
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Affiliation(s)
- Daniel
W. Heindel
- Biomedical
Research Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| | - Shuhui Chen
- Biomedical
Research Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| | - Peter V. Aziz
- SBP
Medical Discovery Institute, La Jolla, California 92037, United States
| | - Jonathan Y. Chung
- Biomedical
Research Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| | - Jamey D. Marth
- SBP
Medical Discovery Institute, La Jolla, California 92037, United States
| | - Lara K. Mahal
- Biomedical
Research Institute, Department of Chemistry, New York University, New York, New York 10003, United States
- Department
of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
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5
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Neu3 neuraminidase induction triggers intestinal inflammation and colitis in a model of recurrent human food-poisoning. Proc Natl Acad Sci U S A 2021; 118:2100937118. [PMID: 34266954 DOI: 10.1073/pnas.2100937118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Intestinal inflammation is the underlying basis of colitis and the inflammatory bowel diseases. These syndromes originate from genetic and environmental factors that remain to be fully identified. Infections are possible disease triggers, including recurrent human food-poisoning by the common foodborne pathogen Salmonella enterica Typhimurium (ST), which in laboratory mice causes progressive intestinal inflammation leading to an enduring colitis. In this colitis model, disease onset has been linked to Toll-like receptor-4-dependent induction of intestinal neuraminidase activity, leading to the desialylation, reduced half-life, and acquired deficiency of anti-inflammatory intestinal alkaline phosphatase (IAP). Neuraminidase (Neu) inhibition protected against disease onset; however, the source and identity of the Neu enzyme(s) responsible remained unknown. Herein, we report that the mammalian Neu3 neuraminidase is responsible for intestinal IAP desialylation and deficiency. Absence of Neu3 thereby prevented the accumulation of lipopolysaccharide-phosphate and inflammatory cytokine expression in providing protection against the development of severe colitis.
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The RD2 Pathogenicity Island Modifies the Disease Potential of the Group A Streptococcus. Infect Immun 2021; 89:e0072220. [PMID: 33820819 DOI: 10.1128/iai.00722-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Serotype M28 isolates of the group A Streptococcus (GAS; Streptococcus pyogenes) are nonrandomly associated with cases of puerperal sepsis, a potentially life-threatening infection that can occur in women following childbirth. Previously, we discovered that the 36.3-kb RD2 pathogenicity island, which is present in serotype M28 isolates but lacking from most other isolates, promotes the ability of M28 GAS to colonize the female reproductive tract. Here, we performed a gain-of-function study in which we introduced RD2 into representative serotype M1, M49, and M59 isolates and assessed the phenotypic consequences of RD2 acquisition. All RD2-containing derivatives colonized a higher percentage of mice, and at higher CFU levels, than did the parental isolates in a mouse vaginal colonization model. However, for two additional phenotypes, survival in heparinized whole human blood and adherence to two human vaginal epithelial cell lines, there were serotype-specific differences from RD2 acquisition. Using transcriptomic comparisons, we identified that such differences may be a consequence of RD2 altering the abundance of transcripts from select core genome genes along serotype-specific lines. Our study is the first that interrogates RD2 function in GAS serotypes other than M28 isolates, shedding light on variability in the phenotypic consequences of RD2 acquisition and informing on why this mobile genetic element is not ubiquitous in the GAS population.
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Parise D, Teixeira Dornelles Parise M, Pinto Gomide AC, Figueira Aburjaile F, Bentes Kato R, Salgado-Albarrán M, Tauch A, Ariston de Carvalho Azevedo V, Baumbach J. The Transcriptional Regulatory Network of Corynebacterium pseudotuberculosis. Microorganisms 2021; 9:microorganisms9020415. [PMID: 33671149 PMCID: PMC7923171 DOI: 10.3390/microorganisms9020415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 12/26/2022] Open
Abstract
Corynebacterium pseudotuberculosis is a Gram-positive, facultative intracellular, pathogenic bacterium that infects several different hosts, yielding serious economic losses in livestock farming. It causes several diseases including oedematous skin disease (OSD) in buffaloes, ulcerative lymphangitis (UL) in horses, and caseous lymphadenitis (CLA) in sheep, goats and humans. Despite its economic and medical-veterinary importance, our understanding concerning this organism’s transcriptional regulatory mechanisms is still limited. Here, we review the state of the art knowledge on transcriptional regulatory mechanisms of this pathogenic species, covering regulatory interactions mediated by two-component systems, transcription factors and sigma factors. Key transcriptional regulatory players involved in virulence and pathogenicity of C. pseudotuberculosis, such as the PhoPR system and DtxR, are in the focus of this review, as these regulators are promising targets for future vaccine design and drug development. We conclude that more experimental studies are needed to further understand the regulatory repertoire of this important zoonotic pathogen, and that regulators are promising targets for future vaccine design and drug development.
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Affiliation(s)
- Doglas Parise
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany; (M.T.D.P.); (M.S.-A.); (J.B.)
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
- Correspondence: or
| | - Mariana Teixeira Dornelles Parise
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany; (M.T.D.P.); (M.S.-A.); (J.B.)
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
| | - Anne Cybelle Pinto Gomide
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
| | | | - Rodrigo Bentes Kato
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
| | - Marisol Salgado-Albarrán
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany; (M.T.D.P.); (M.S.-A.); (J.B.)
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana Cuajimalpa, Mexico City 05348, Mexico
| | - Andreas Tauch
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany;
| | - Vasco Ariston de Carvalho Azevedo
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; (A.C.P.G.); (R.B.K.); (V.A.d.C.A.)
| | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany; (M.T.D.P.); (M.S.-A.); (J.B.)
- Computational BioMedicine lab, Institute of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
- Chair of Computational Systems Biology, University of Hamburg, 22607 Hamburg, Germany
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8
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Pradhan D, Pradhan J, Mishra A, Karmakar K, Dhiman R, Chakravortty D, Negi VD. Immune modulations and survival strategies of evolved hypervirulent Salmonella Typhimurium strains. Biochim Biophys Acta Gen Subj 2020; 1864:129627. [PMID: 32360143 DOI: 10.1016/j.bbagen.2020.129627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/19/2020] [Accepted: 04/24/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND Evolving multidrug-resistance and hypervirulence in Salmonella is due to multiple host-pathogen, and non-host environmental interactions. Previously we had studied Salmonella adaptation upon repeated exposure in different in-vitro and in-vivo environmental conditions. This study deals with the mechanistic basis of hypervirulence of the passaged hypervirulent Salmonella strains reported previously. METHODS Real-time PCR, flow cytometry, western blotting, and confocal microscopy were employed to check the alteration of signaling pathways by the hypervirulent strains. The hypervirulence was also looked in-vivo in the Balb/c murine model system. RESULTS The hypervirulent strains altered cytokine production towards anti-inflammatory response via NF-κB and Akt-NLRC4 signaling in RAW-264.7 and U-937 cells. They also impaired lysosome number, as well as co-localization with the lysosome as compared to unpassaged WT-STM. In Balb/c mice also they caused decreased antimicrobial peptides, reduced nitric oxide level, altered cytokine production, and reduced CD4+ T cell population leading to increased organ burden. CONCLUSIONS Hypervirulent Salmonella strains infection resulted in an anti-inflammatory environment by upregulating IL-10 and down-regulating IL-1β expression. They also evaded lysosomal degradation for their survival. With inhibition of NF-κB and Akt signaling, cytokine expression, lysosome number, as well as the bacterial burden was reverted, indicating the infection mediated immune modulation by the hypervirulent Salmonella strains through these pathways. GENERAL SIGNIFICANCE Understanding the mechanism of adaptation can provide better disease prognosis by either targeting the bacterial gene or by strengthening the host immune system that might ultimately help in controlling salmonellosis.
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Affiliation(s)
- Diana Pradhan
- Laboratory of Infection Immunology, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Jasmin Pradhan
- Laboratory of Infection Immunology, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Abtar Mishra
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Kapudeep Karmakar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India; Regional Research Station, Terai Zone, Uttar Banga Krishi Viswavidyalaya, Coochbehar, west Bengal 736165, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Vidya Devi Negi
- Laboratory of Infection Immunology, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India.
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9
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Bandoy DJDR, Weimer BC. Biological Machine Learning Combined with Campylobacter Population Genomics Reveals Virulence Gene Allelic Variants Cause Disease. Microorganisms 2020; 8:E549. [PMID: 32290186 PMCID: PMC7232492 DOI: 10.3390/microorganisms8040549] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 01/17/2023] Open
Abstract
Highly dimensional data generated from bacterial whole-genome sequencing is providing an unprecedented scale of information that requires an appropriate statistical analysis framework to infer biological function from populations of genomes. The application of genome-wide association study (GWAS) methods is an appropriate framework for bacterial population genome analysis that yields a list of candidate genes associated with a phenotype, but it provides an unranked measure of importance. Here, we validated a novel framework to define infection mechanism using the combination of GWAS, machine learning, and bacterial population genomics that ranked allelic variants that accurately identified disease. This approach parsed a dataset of 1.2 million single nucleotide polymorphisms (SNPs) and indels that resulted in an importance ranked list of associated alleles of porA in Campylobacter jejuni using spatiotemporal analysis over 30 years. We validated this approach using previously proven laboratory experimental alleles from an in vivo guinea pig abortion model. This framework, termed µPathML, defined intestinal and extraintestinal groups that have differential allelic porA variants that cause abortion. Divergent variants containing indels that defeated automated annotation were rescued using biological context and knowledge that resulted in defining rare, divergent variants that were maintained in the population over two continents and 30 years. This study defines the capability of machine learning coupled with GWAS and population genomics to simultaneously identify and rank alleles to define their role in infectious disease mechanisms.
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Affiliation(s)
- DJ Darwin R. Bandoy
- 100 K Pathogen Genome Project, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
- Department of Veterinary, Paraclinical Sciences, College of Veterinary Medicine, University of the Philippines Los Baños, Los Baños 4031, Philippines;
| | - Bart C. Weimer
- 100 K Pathogen Genome Project, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
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10
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Affiliation(s)
- Marie-Stéphanie Aschtgen
- From the, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Lee Kong Chian School of Medicine (LKC), Singapore Centre on Environmental LifeSciences Engineering (SCELSE), Nanyang Technological University, Singapore City, Singapore
| | - Birgitta Henriques-Normark
- From the, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Lee Kong Chian School of Medicine (LKC), Singapore Centre on Environmental LifeSciences Engineering (SCELSE), Nanyang Technological University, Singapore City, Singapore.,Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Staffan Normark
- From the, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Lee Kong Chian School of Medicine (LKC), Singapore Centre on Environmental LifeSciences Engineering (SCELSE), Nanyang Technological University, Singapore City, Singapore.,Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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11
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Stress-induced adaptations in Salmonella: A ground for shaping its pathogenesis. Microbiol Res 2019; 229:126311. [DOI: 10.1016/j.micres.2019.126311] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 12/12/2022]
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12
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Pradhan D, Negi VD. Repeated in-vitro and in-vivo exposure leads to genetic alteration, adaptations, and hypervirulence in Salmonella. Microb Pathog 2019; 136:103654. [DOI: 10.1016/j.micpath.2019.103654] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 11/30/2022]
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13
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Chiok KLR, Shah DH. Identification of common highly expressed genes of Salmonella Enteritidis by in silico prediction of gene expression and in vitro transcriptomic analysis. Poult Sci 2019; 98:2948-2963. [PMID: 30953073 DOI: 10.3382/ps/pez119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/27/2019] [Indexed: 01/02/2023] Open
Abstract
Chickens are the reservoir host of Salmonella Enteritidis. Salmonella Enteritidis colonizes the gastro-intestinal tract of chickens and replicates within macrophages without causing clinically discernable illness. Persistence of S. Enteritidis in the hostile environments of intestinal tract and macrophages allows it to disseminate extra-intestinally to liver, spleen, and reproductive tract. Extra-intestinal dissemination into reproductive tract leads to contamination of internal contents of eggs, which is a major risk factor for human infection. Understanding the genes that contribute to S. Enteritidis persistence in the chicken host is central to elucidate the genetic basis of the unique pathobiology of this public health pathogen. The aim of this study was to identify a succinct set of genes associated with infection-relevant in vitro environments to provide a rational foundation for subsequent biologically-relevant research. We used in silico prediction of gene expression and RNA-seq technology to identify a core set of 73 S. Enteritidis genes that are consistently highly expressed in multiple S. Enteritidis strains cultured at avian physiologic temperature under conditions that represent intestinal and intracellular environments. These common highly expressed (CHX) genes encode proteins involved in bacterial metabolism, protein synthesis, cell-envelope biogenesis, stress response, and a few proteins with uncharacterized functions. Further studies are needed to dissect the contribution of these CHX genes to the pathobiology of S. Enteritidis in the avian host. Several of the CHX genes could serve as promising targets for studies towards the development of immunoprophylactic and novel therapeutic strategies to prevent colonization of chickens and their environment with S. Enteritidis.
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Affiliation(s)
- Kim Lam R Chiok
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164-7040
| | - Devendra H Shah
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164-7040
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14
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The Salmonella virulence protein MgtC promotes phosphate uptake inside macrophages. Nat Commun 2019; 10:3326. [PMID: 31346161 PMCID: PMC6658541 DOI: 10.1038/s41467-019-11318-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 07/05/2019] [Indexed: 02/06/2023] Open
Abstract
The MgtC virulence protein from the intracellular pathogen Salmonella enterica is required for its intramacrophage survival and virulence in mice and this requirement of MgtC is conserved in several intracellular pathogens including Mycobacterium tuberculosis. Despite its critical role in survival within macrophages, only a few molecular targets of the MgtC protein have been identified. Here, we report that MgtC targets PhoR histidine kinase and activates phosphate transport independently of the available phosphate concentration. A single amino acid substitution in PhoR prevents its binding to MgtC, thus abrogating MgtC-mediated phosphate transport. Surprisingly, the removal of MgtC’s effect on the ability to transport phosphate renders Salmonella hypervirulent and decreases a non-replicating population inside macrophages, indicating that MgtC-mediated phosphate transport is required for normal Salmonella pathogenesis. This provides an example of a virulence protein directly activating a pathogen’s phosphate transport inside host. The virulence factor MgtC is essential for intracellular macrophage survival of Salmonella enterica. Here, the authors show that MgtC targets the PhoB/PhoR regulatory system leading to phosphate uptake inside macrophages and that both phoR mutation and phoB deletion renders Salmonella hypervirulent in mice.
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15
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Yang WH, Heithoff DM, Aziz PV, Haslund-Gourley B, Westman JS, Narisawa S, Pinkerton AB, Millán JL, Nizet V, Mahan MJ, Marth JD. Accelerated Aging and Clearance of Host Anti-inflammatory Enzymes by Discrete Pathogens Fuels Sepsis. Cell Host Microbe 2019; 24:500-513.e5. [PMID: 30308156 DOI: 10.1016/j.chom.2018.09.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/09/2018] [Accepted: 09/16/2018] [Indexed: 12/29/2022]
Abstract
Sepsis is a life-threatening inflammatory syndrome accompanying a bloodstream infection. Frequently secondary to pathogenic bacterial infections, sepsis remains difficult to treat as a singular disease mechanism. We compared the pathogenesis of murine sepsis experimentally elicited by five bacterial pathogens and report similarities among host responses to Gram-negative Salmonella and E. coli. We observed that a host protective mechanism involving de-toxification of lipopolysaccharide by circulating alkaline phosphatase (AP) isozymes was incapacitated during sepsis caused by Salmonella or E. coli through activation of host Toll-like receptor 4, which triggered Neu1 and Neu3 neuraminidase induction. Elevated neuraminidase activity accelerated the molecular aging and clearance of AP isozymes, thereby intensifying disease. Mice deficient in the sialyltransferase ST3Gal6 displayed increased disease severity, while deficiency of the endocytic lectin hepatic Ashwell-Morell receptor was protective. AP augmentation or neuraminidase inhibition diminished inflammation and promoted host survival. This study illuminates distinct routes of sepsis pathogenesis, which may inform therapeutic development.
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Affiliation(s)
- Won Ho Yang
- Center for Nanomedicine, University of California Santa Barbara, Santa Barbara, California 93106, USA; Sanford-Burham-Prebys Medical Discovery Institute, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Douglas M Heithoff
- Center for Nanomedicine, University of California Santa Barbara, Santa Barbara, California 93106, USA; Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Peter V Aziz
- Center for Nanomedicine, University of California Santa Barbara, Santa Barbara, California 93106, USA; Sanford-Burham-Prebys Medical Discovery Institute, University of California Santa Barbara, Santa Barbara, California 93106, USA; Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Benjamin Haslund-Gourley
- Center for Nanomedicine, University of California Santa Barbara, Santa Barbara, California 93106, USA; Sanford-Burham-Prebys Medical Discovery Institute, University of California Santa Barbara, Santa Barbara, California 93106, USA; Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Julia S Westman
- Center for Nanomedicine, University of California Santa Barbara, Santa Barbara, California 93106, USA; Sanford-Burham-Prebys Medical Discovery Institute, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Sonoko Narisawa
- Sanford-Burham-Prebys Medical Discovery Institute, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Anthony B Pinkerton
- Sanford-Burham-Prebys Medical Discovery Institute, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - José Luis Millán
- Sanford-Burham-Prebys Medical Discovery Institute, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Victor Nizet
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Michael J Mahan
- Center for Nanomedicine, University of California Santa Barbara, Santa Barbara, California 93106, USA; Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Jamey D Marth
- Center for Nanomedicine, University of California Santa Barbara, Santa Barbara, California 93106, USA; Sanford-Burham-Prebys Medical Discovery Institute, University of California Santa Barbara, Santa Barbara, California 93106, USA; Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California 93106, USA.
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16
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Bosilevac JM, Zhilyaev S, Wang R, Luedtke BE, Wheeler TL, Koohmaraie M. Prevalence and Characterization of Salmonella Present during Veal Harvest. J Food Prot 2019; 82:775-784. [PMID: 30986365 DOI: 10.4315/0362-028x.jfp-18-478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Beef and veal products have been vehicles implicated in the transmission of Salmonella enterica, a gastroenteritis-causing bacteria. Recent regulatory samples collected from veal have indicated bob veal, or calves harvested within days of birth, have higher rates of Salmonella than samples collected from formula-fed veal, or calves raised 20 weeks on milk replacer formula before harvest. To investigate this problem, we collected samples from veal calf hides, preevisceration carcasses, and final carcasses at five veal processors that harvested bob or formula-fed veal or both. Prevalence and concentrations of Salmonella were determined, and then the isolates were characterized for serovar and antibiotic susceptibility. Salmonella was more prevalent (P < 0.05) among bob veal than formula-fed veal hides, preevisceration carcasses, and final carcass (84.2 versus 15.6%, 62.8 versus 10.1%, and 12.0 versus 0.4%, respectively). Concentrations of Salmonella could be estimated by using regression order statistics on hides and preevisceration carcasses at two veal plants, with one harvesting bob veal and the other bob and formula-fed veal. The concentration of Salmonella on bob veal hides at the plants was 1.45 ± 0.70 and 2.04 ± 1.00 log CFU/100 cm2, greater (P < 0.05) than on formula-fed veal hides, which was 1.10 ± 1.51 log CFU/100 cm2. Concentrations on carcasses, however, were very low. Seventeen Salmonella serovars were identified among 710 isolates. Salmonella serovars London, Cerro, and Muenster were most common to bob veal and made up 50.7, 18.7, and 6.3% of the isolates, respectively, while serovar Montevideo (6.8% of isolates) was most common to formula-fed veal. Although bob veal had increased prevalence and concentrations of Salmonella, one group of formula-fed veal was found to harbor human disease-related antibiotic-resistant Salmonella serovars Heidelberg and the monophasic variant of Typhimurium (1,4,[5],12:i:-). Veal processors have made changes to improve the safety of veal, but further efforts are necessary from both bob and formula-fed veal to address Salmonella.
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Affiliation(s)
- Joseph M Bosilevac
- 1 U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933 (ORCID: https://orcid.org/0000-0002-0258-6581 [J.M.B.]; https://orcid.org/0000-0003-1924-3275 [R.W.]; https://orcid.org/0000-0002-6571-9097 [T.L.W.])
| | - Samson Zhilyaev
- 2 Virginia Polytechnic Institute and State University, 1145 Perry Street, Blacksburg, Virginia 24061
| | - Rong Wang
- 1 U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933 (ORCID: https://orcid.org/0000-0002-0258-6581 [J.M.B.]; https://orcid.org/0000-0003-1924-3275 [R.W.]; https://orcid.org/0000-0002-6571-9097 [T.L.W.])
| | - Brandon E Luedtke
- 3 University of Nebraska Kearney, 2401 11th Avenue, Kearney, Nebraska 68849 (ORCID: https://orcid.org/0000-0003-3349-3270 [B.E.L.])
| | - Tommy L Wheeler
- 1 U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933 (ORCID: https://orcid.org/0000-0002-0258-6581 [J.M.B.]; https://orcid.org/0000-0003-1924-3275 [R.W.]; https://orcid.org/0000-0002-6571-9097 [T.L.W.])
| | - Mohammad Koohmaraie
- 4 IEH Laboratories and Consulting Group, 15300 Bothell Way N.E., Lake Forest Park, Washington 98155, USA
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17
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Foods NACOMCF. Response to Questions Posed by the Food Safety and Inspection Service Regarding Salmonella Control Strategies in Poultry †. J Food Prot 2019; 82:645-668. [PMID: 30917043 DOI: 10.4315/0362-028x.jfp-18-500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Antaki-Zukoski EM, Li X, Pesavento PA, Nguyen THB, Hoar BR, Atwill ER. Comparative Pathogenicity of Wildlife and Bovine Escherichia coli O157:H7 Strains in Experimentally Inoculated Neonatal Jersey Calves. Vet Sci 2018; 5:E88. [PMID: 30326606 PMCID: PMC6313898 DOI: 10.3390/vetsci5040088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 11/23/2022] Open
Abstract
Shiga toxin-producing Escherichia coli, like E. coli O157:H7, are important human and animal pathogens. Naturally-acquired E. coli O157:H7 infections occur in numerous species but, particularly, cattle have been identified as a significant reservoir for human cases. E. coli O157:H7 are isolated from a number of domestic and wild animals, including rodents that share a living space with cattle. These Shiga toxin-producing E. coli O157:H7 strains can be highly virulent in humans, but little is known about the sequelae of interspecies transfer. In a group of neonatal calves, we determined the differences in colonization patterns and lesions associated with infection using either a wildlife or bovine E. coli O157:H7 strain. In calves challenged with the wildlife E. coli O157:H7 strain, the large (descending) colon was solely colonized, which differed substantially from the calves inoculated with the bovine E. coli O157:H7 strain, where the spiral colon was the principal target of infection. This study also demonstrated that while both interspecies- and intraspecies-derived E. coli O157:H7 can infect young calves, the distribution and severity differs.
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Affiliation(s)
- Elizabeth M Antaki-Zukoski
- Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA.
- Western Institute for Food Safety and Security, University of California, Davis, CA 95618, USA.
| | - Xunde Li
- Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA.
- Western Institute for Food Safety and Security, University of California, Davis, CA 95618, USA.
| | - Patricia A Pesavento
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA.
| | - Tran H B Nguyen
- Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA.
| | - Bruce R Hoar
- College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY 82071, USA.
| | - Edward R Atwill
- Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA.
- Western Institute for Food Safety and Security, University of California, Davis, CA 95618, USA.
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19
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Smartphone-based pathogen diagnosis in urinary sepsis patients. EBioMedicine 2018; 36:73-82. [PMID: 30245056 PMCID: PMC6197494 DOI: 10.1016/j.ebiom.2018.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/01/2018] [Accepted: 09/03/2018] [Indexed: 11/22/2022] Open
Abstract
Background There is an urgent need for rapid, sensitive, and affordable diagnostics for microbial infections at the point-of-care. Although a number of innovative systems have been reported that transform mobile phones into potential diagnostic tools, the translational challenge to clinical diagnostics remains a significant hurdle to overcome. Methods A smartphone-based real-time loop-mediated isothermal amplification (smaRT-LAMP) system was developed for pathogen ID in urinary sepsis patients. The free, custom-built mobile phone app allows the phone to serve as a stand-alone device for quantitative diagnostics, allowing the determination of genome copy-number of bacterial pathogens in real time. Findings A head-to-head comparative bacterial analysis of urine from sepsis patients revealed that the performance of smaRT-LAMP matched that of clinical diagnostics at the admitting hospital in a fraction of the time (~1 h vs. 18–28 h). Among patients with bacteremic complications of their urinary sepsis, pathogen ID from the urine matched that from the blood – potentially allowing pathogen diagnosis shortly after hospital admission. Additionally, smaRT-LAMP did not exhibit false positives in sepsis patients with clinically negative urine cultures. Interpretation The smaRT-LAMP system is effective against diverse Gram-negative and -positive pathogens and biological specimens, costs less than $100 US to fabricate (in addition to the smartphone), and is configurable for the simultaneous detection of multiple pathogens. SmaRT-LAMP thus offers the potential to deliver rapid diagnosis and treatment of urinary tract infections and urinary sepsis with a simple test that can be performed at low cost at the point-of-care. Fund National Institutes of Health, Chan-Zuckerberg Biohub, Bill and Melinda Gates Foundation.
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20
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Weimer BC, Chen P, Desai PT, Chen D, Shah J. Whole Cell Cross-Linking to Discover Host-Microbe Protein Cognate Receptor/Ligand Pairs. Front Microbiol 2018; 9:1585. [PMID: 30072965 PMCID: PMC6060266 DOI: 10.3389/fmicb.2018.01585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 06/26/2018] [Indexed: 12/31/2022] Open
Abstract
Bacterial surface ligands mediate interactions with the host cell during association that determines the specific outcome for the host–microbe association. The association begins with receptors on the host cell binding ligands on the microbial cell to form a partnership that initiates responses in both cells. Methods to determine the specific cognate partnerships are lacking. Determining these molecular interactions between the host and microbial surfaces are difficult, yet crucial in defining biologically important events that are triggered during association of the microbiome, and critical in defining the initiating signal from the host membrane that results in pathology or commensal association. In this study, we designed an approach to discover cognate host–microbe receptor/ligand pairs using a covalent cross-linking strategy with whole cells. Protein/protein cross-linking occurred when the interacting molecules were within 9–12 Å, allowing for identification of specific pairs of proteins from the host and microbe that define the molecular interaction during association. To validate the method three different bacteria with three previously known protein/protein partnerships were examined. The exact interactions were confirmed and led to discovery of additional partnerships that were not recognized as cognate partners, but were previously reported to be involved in bacterial interactions. Additionally, three unknown receptor/ligand partners were discovered and validated with in vitro infection assays by blocking the putative host receptor and deleting the bacterial ligand. Subsequently, Salmonella enterica sv. Typhimurium was cross-linked to differentiated colonic epithelial cells (caco-2) to discover four previously unknown host receptors bound to three previously undefined host ligands for Salmonella. This approach resulted in a priori discovery of previously unknown and biologically important molecules for host/microbe association that were casually reported to mediate bacterial invasion. The whole cell cross-linking approach promises to enable discovery of possible targets to modulate interaction of the microbiome with the host that are important in infection and commensalism, both of with initiate a host response.
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Affiliation(s)
- Bart C Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Poyin Chen
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Prerak T Desai
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.,Department of Dietetics, Nutrition and Food Sciences, Utah State University, Logan, UT, United States
| | - Dong Chen
- Department of Biology, Utah State University, Logan, UT, United States
| | - Jigna Shah
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.,Department of Dietetics, Nutrition and Food Sciences, Utah State University, Logan, UT, United States
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21
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Ricke SC, Dawoud TM, Kim SA, Park SH, Kwon YM. Salmonella Cold Stress Response: Mechanisms and Occurrence in Foods. ADVANCES IN APPLIED MICROBIOLOGY 2018; 104:1-38. [PMID: 30143250 DOI: 10.1016/bs.aambs.2018.03.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Since bacteria in foods often encounter various cold environments during food processing, such as chilling, cold chain distribution, and cold storage, lower temperatures can become a major stress environment for foodborne pathogens. Bacterial responses in stressful environments have been considered in the past, but now the importance of stress responses at the molecular level is becoming recognized. Documenting how bacterial changes occur at the molecular level may help to achieve the in-depth understanding of stress responses, to predict microbial fate when they encounter cold temperatures, and to design and develop more effective strategies to control pathogens in food for ensuring food safety. Microorganisms differ in responding to a sudden downshift in temperature and this, in turn, impacts their metabolic processes and can cause various structural modifications. In this review, the fundamental aspects of bacterial cold stress responses focused on cell membrane modification, DNA supercoiling modification, transcriptional and translational responses, cold-induced protein synthesis including CspA, CsdA, NusA, DnaA, RecA, RbfA, PNPase, KsgA, SrmB, trigger factors, and initiation factors are discussed. In this context, specific Salmonella responses to cold temperature including growth, injury, and survival and their physiological and genetic responses to cold environments with a focus on cross-protection, different gene expression levels, and virulence factors will be discussed.
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Affiliation(s)
- Steven C Ricke
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States; Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Food Science, University of Arkansas, Fayetteville, AR, United States.
| | - Turki M Dawoud
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States; Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Sun Ae Kim
- Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Food Science, University of Arkansas, Fayetteville, AR, United States; Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Si Hong Park
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States; Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Young Min Kwon
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States; Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
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22
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Murray K, Tremblay C, Rghei A, Warriner K. Challenges and options for enhancing Salmonella control in partially cooked breaded poultry products. Curr Opin Food Sci 2018. [DOI: 10.1016/j.cofs.2018.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Yang WH, Heithoff DM, Aziz PV, Sperandio M, Nizet V, Mahan MJ, Marth JD. Recurrent infection progressively disables host protection against intestinal inflammation. Science 2018; 358:358/6370/eaao5610. [PMID: 29269445 DOI: 10.1126/science.aao5610] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/13/2017] [Indexed: 12/15/2022]
Abstract
Intestinal inflammation is the central pathological feature of colitis and the inflammatory bowel diseases. These syndromes arise from unidentified environmental factors. We found that recurrent nonlethal gastric infections of Gram-negative Salmonella enterica Typhimurium (ST), a major source of human food poisoning, caused inflammation of murine intestinal tissue, predominantly the colon, which persisted after pathogen clearance and irreversibly escalated in severity with repeated infections. ST progressively disabled a host mechanism of protection by inducing endogenous neuraminidase activity, which accelerated the molecular aging and clearance of intestinal alkaline phosphatase (IAP). Disease was linked to a Toll-like receptor 4 (TLR4)-dependent mechanism of IAP desialylation with accumulation of the IAP substrate and TLR4 ligand, lipopolysaccharide-phosphate. The administration of IAP or the antiviral neuraminidase inhibitor zanamivir was therapeutic by maintaining IAP abundance and function.
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Affiliation(s)
- Won Ho Yang
- Center for Nanomedicine, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.,Sanford Burnham Prebys Medical Discovery Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.,Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Douglas M Heithoff
- Center for Nanomedicine, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.,Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Peter V Aziz
- Center for Nanomedicine, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.,Sanford Burnham Prebys Medical Discovery Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.,Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Markus Sperandio
- Walter-Brendel-Centre for Experimental Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Victor Nizet
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael J Mahan
- Center for Nanomedicine, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.,Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Jamey D Marth
- Center for Nanomedicine, University of California, Santa Barbara, Santa Barbara, CA 93106, USA. .,Sanford Burnham Prebys Medical Discovery Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.,Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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Identification and Characterization of Serotype-Specific Variation in Group A Streptococcus Pilus Expression. Infect Immun 2018; 86:IAI.00792-17. [PMID: 29158432 DOI: 10.1128/iai.00792-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 11/13/2017] [Indexed: 12/22/2022] Open
Abstract
Isolates of a given bacterial pathogen often display phenotypic variation, and this can negatively impact public health, for example, by reducing the efficacy of preventative measures. Here, we identify that the human pathogen group A Streptococcus (GAS; Streptococcus pyogenes) expresses pili on its cell surface in a serotype-specific manner. Specifically, we show that serotype M3 GAS isolates, which are nonrandomly associated with causing particularly severe and lethal invasive infections, produce negligible amounts of pili relative to serotype M1 and M49 isolates. Performance of an interserotype transcriptome comparison (serotype M1 versus serotype M3) was instrumental in this discovery. We also identified that the transcriptional regulator Nra positively regulates pilus expression in M3 GAS isolates and that the low level of pilus expression of these isolates correlates with a low level of nra transcription. Finally, we discovered that the phenotypic consequences of low levels of pilus expression by M3 GAS isolates are a reduced ability to adhere to host cells and an increased ability to survive and proliferate in human blood. We propose that an enhanced ability to survive in human blood, in part due to reduced pilus expression, is a contributing factor in the association of serotype M3 isolates with highly invasive infections. In conclusion, our data show that GAS isolates express pili in a serotype-dependent manner and may inform vaccine development, given that pilus proteins are being discussed as possible GAS vaccine antigens.
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RocA Is an Accessory Protein to the Virulence-Regulating CovRS Two-Component System in Group A Streptococcus. Infect Immun 2017; 85:IAI.00274-17. [PMID: 28808155 DOI: 10.1128/iai.00274-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/05/2017] [Indexed: 11/20/2022] Open
Abstract
Regulating gene expression during infection is critical to the ability of pathogens to circumvent the immune response and cause disease. This is true for the group A Streptococcus (GAS), a pathogen that causes both invasive (e.g., necrotizing fasciitis) and noninvasive (e.g., pharyngitis) diseases. The control of virulence (CovRS) two-component system has a major role in regulating GAS virulence factor expression. The regulator of cov (RocA) protein, which is a predicted kinase, functions in an undetermined manner through CovRS to alter gene expression and reduce invasive disease virulence. Here, we show that the ectopic expression of a truncated RocA derivative, harboring the membrane-spanning domains but not the dimerization or HATPase domain, is sufficient to complement a rocA mutant strain. Coupled with a previous bioinformatic study, the data are consistent with RocA being a pseudokinase. RocA reduces the ability of serotype M1 GAS isolates to express capsule and to evade killing in human blood, phenotypes that are not observed for M3 or M18 GAS due to isolates of these serotypes naturally harboring mutant rocA alleles. In addition, we found that varying the RocA concentration attenuates the regulatory activity of Mg2+ and the antimicrobial peptide LL-37, which positively and negatively regulate CovS function, respectively. Thus, we propose that RocA is an accessory protein to the CovRS system that influences the ability of GAS to modulate gene expression in response to host factors. A model of how RocA interacts with CovRS, and of the regulatory consequences of such activity, is presented.
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26
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Papizadeh M, Rohani M, Nahrevanian H, Javadi A, Pourshafie MR. Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends. Microb Pathog 2017; 111:118-131. [DOI: 10.1016/j.micpath.2017.08.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/12/2017] [Accepted: 08/16/2017] [Indexed: 02/07/2023]
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27
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Shelby T, Sulthana S, McAfee J, Banerjee T, Santra S. Foodborne Pathogen Screening Using Magneto-fluorescent Nanosensor: Rapid Detection of E. Coli O157:H7. J Vis Exp 2017. [PMID: 28994755 DOI: 10.3791/55821] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Enterohemorrhagic Escherichia coli O157:H7 has been linked to both waterborne and foodborne illnesses, and remains a threat despite the food- and water-screening methods used currently. While conventional bacterial detection methods, such as polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA) can specifically detect pathogenic contaminants, they require extensive sample preparation and lengthy waiting periods. In addition, these practices demand sophisticated laboratory instruments and settings, and must be executed by trained professionals. Herein, a protocol is proposed for a simpler diagnostic technique that features the unique combination of magnetic and fluorescent parameters in a nanoparticle-based platform. The proposed multiparametric magneto-fluorescent nanosensors (MFnS) can detect E. coli O157:H7 contamination with as little as 1 colony-forming unit present in solution within less than 1 h. Furthermore, the ability of MFnS to remain highly functional in complex media such as milk and lake water has been verified. Additional specificity assays were also used to demonstrate the ability of MFnS to only detect the specific target bacteria, even in the presence of similar bacterial species. The pairing of magnetic and fluorescent modalities allows for the detection and quantification of pathogen contamination in a wide range of concentrations, exhibiting its high performance in both early- and late-stage contamination detection. The effectiveness, affordability, and portability of the MFnS make them an ideal candidate for point-of-care screening for bacterial contaminants in a wide range of settings, from aquatic reservoirs to commercially packaged foods.
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Affiliation(s)
- Tyler Shelby
- Department of Chemistry and Kansas Polymer Research Center, Pittsburg State University
| | - Shoukath Sulthana
- Department of Chemistry and Kansas Polymer Research Center, Pittsburg State University
| | - James McAfee
- Department of Chemistry and Kansas Polymer Research Center, Pittsburg State University
| | - Tuhina Banerjee
- Department of Chemistry and Kansas Polymer Research Center, Pittsburg State University;
| | - Santimukul Santra
- Department of Chemistry and Kansas Polymer Research Center, Pittsburg State University;
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Draft Genome Sequences of 1,183 Salmonella Strains from the 100K Pathogen Genome Project. GENOME ANNOUNCEMENTS 2017; 5:5/28/e00518-17. [PMID: 28705963 PMCID: PMC5511902 DOI: 10.1128/genomea.00518-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Salmonella is a common food-associated bacterium that has substantial impact on worldwide human health and the global economy. This is the public release of 1,183 Salmonella draft genome sequences as part of the 100K Pathogen Genome Project. These isolates represent global genomic diversity in the Salmonella genus.
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Chylkova T, Cadena M, Ferreiro A, Pitesky M. Susceptibility of Salmonella Biofilm and Planktonic Bacteria to Common Disinfectant Agents Used in Poultry Processing. J Food Prot 2017; 80:1072-1079. [PMID: 28561639 DOI: 10.4315/0362-028x.jfp-16-393] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Poultry contaminated with Salmonella enterica subsp. enterica are a major cause of zoonotic foodborne gastroenteritis. Salmonella Heidelberg is a common serotype of Salmonella that has been implicated as a foodborne pathogen associated with the consumption of improperly prepared chicken. To better understand the effectiveness of common antimicrobial disinfectants (i.e., peroxyacetic acid [PAA], acidified hypochlorite [aCH], and cetylpyridinium chloride [CPC]), environmental isolates of nontyphoidal Salmonella were exposed to these agents under temperature, concentration, and contact time conditions consistent with poultry processing. Under simulated processing conditions (i.e., chiller tank and dipping stations), the bacteriostatic and bactericidal effects of each disinfectant were assessed against biofilm and planktonic cultures of each organism in a disinfectant challenge. Log reductions, planktonic MICs, and mean biofilm eradication concentrations were computed. The biofilms of each Salmonella isolate were more resistant to the disinfectants than were their planktonic counterparts. Although PAA was bacteriostatic and bactericidal against the biofilm and planktonic Salmonella isolates tested at concentrations up to 64 times the concentrations commonly used in a chiller tank during poultry processing, aCH was ineffective against the same isolates under identical conditions. At the simulated 8-s dipping station, CPC was bacteriostatic against all seven and bactericidal against six of the seven Salmonella isolates in their biofilm forms at concentrations within the regulatory range. These results indicate that at the current contact times and concentrations, aCH and PAA are not effective against these Salmonella isolates in their biofilm state. The use of CPC should be considered as a tool for controlling Salmonella biofilms in poultry processing environments.
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Affiliation(s)
- Tereza Chylkova
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Myrna Cadena
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Aura Ferreiro
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
| | - Maurice Pitesky
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, One Shields Avenue, Davis, California 95616, USA
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Ersoy SC, Heithoff DM, Barnes L, Tripp GK, House JK, Marth JD, Smith JW, Mahan MJ. Correcting a Fundamental Flaw in the Paradigm for Antimicrobial Susceptibility Testing. EBioMedicine 2017; 20:173-181. [PMID: 28579300 PMCID: PMC5478264 DOI: 10.1016/j.ebiom.2017.05.026] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/20/2017] [Accepted: 05/23/2017] [Indexed: 12/25/2022] Open
Abstract
The emergence and prevalence of antibiotic-resistant bacteria are an increasing cause of death worldwide, resulting in a global ‘call to action’ to avoid receding into an era lacking effective antibiotics. Despite the urgency, the healthcare industry still relies on a single in vitro bioassay to determine antibiotic efficacy. This assay fails to incorporate environmental factors normally present during host-pathogen interactions in vivo that significantly impact antibiotic efficacy. Here we report that standard antimicrobial susceptibility testing (AST) failed to detect antibiotics that are in fact effective in vivo; and frequently identified antibiotics that were instead ineffective as further confirmed in mouse models of infection and sepsis. Notably, AST performed in media mimicking host environments succeeded in identifying specific antibiotics that were effective in bacterial clearance and host survival, even though these same antibiotics failed in results using standard test media. Similarly, our revised media further identified antibiotics that were ineffective in vivo despite passing the AST standard for clinical use. Supplementation of AST medium with sodium bicarbonate, an abundant in vivo molecule that stimulates global changes in bacterial structure and gene expression, was found to be an important factor improving the predictive value of AST in the assignment of appropriate therapy. These findings have the potential to improve the means by which antibiotics are developed, tested, and prescribed. Standard antimicrobial susceptibility testing (AST) is fundamentally flawed because it is based largely on in vitro efficacy. AST performed under conditions that mimic natural infections improves the assignment of appropriate antibiotic therapy. In vivo altered susceptibility (IVAS) provides a new paradigm for drug discovery and therapeutic intervention.
Drug testing often excludes potent antibiotics for the treatment of bacterial infections, while frequently identifying antibiotics that are ineffective. However, drug testing under conditions that mimic natural infections succeeded in identifying effective antibiotics, even though these same antibiotics failed standard tests. This work suggests that standard drug-testing may be hindering patient treatment and slowing the process of discovery of new, effective, and safe antibiotics because it disqualifies effective compounds. These findings call for an overhaul of standardized drug testing which hasn't changed in > 50 years.
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Affiliation(s)
- Selvi C Ersoy
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Douglas M Heithoff
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; Center for Nanomedicine, University of California, Santa Barbara, CA 93106, USA
| | - Lucien Barnes
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Geneva K Tripp
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - John K House
- University of Sydney, Faculty of Veterinary Science, Camden, New South Wales, Australia
| | - Jamey D Marth
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; Center for Nanomedicine, University of California, Santa Barbara, CA 93106, USA; Sanford Burnham Prebys Medical Discovery Institute, Cancer Research Center, La Jolla, CA 92037, USA
| | - Jeffrey W Smith
- Sanford Burnham Prebys Medical Discovery Institute, Cancer Research Center, La Jolla, CA 92037, USA
| | - Michael J Mahan
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; Center for Nanomedicine, University of California, Santa Barbara, CA 93106, USA.
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Draper JL, Hansen LM, Bernick DL, Abedrabbo S, Underwood JG, Kong N, Huang BC, Weis AM, Weimer BC, van Vliet AHM, Pourmand N, Solnick JV, Karplus K, Ottemann KM. Fallacy of the Unique Genome: Sequence Diversity within Single Helicobacter pylori Strains. mBio 2017; 8:e02321-16. [PMID: 28223462 PMCID: PMC5358919 DOI: 10.1128/mbio.02321-16] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 01/30/2017] [Indexed: 12/30/2022] Open
Abstract
Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number. The cagA gene was found as 1 to 4 tandem copies located off the cag island in both SS1 and PMSS1; this copy number variation correlated with protein expression. To gain insight into the changes that occurred during mouse adaptation, we also compared SS1 and PMSS1 and observed 46 differences that were distinct from the within-genome variation. The most substantial was an insertion in cagY, which encodes a protein required for a type IV secretion system function. We detected modifications in genes coding for two proteins known to affect mouse colonization, the HpaA neuraminyllactose-binding protein and the FutB α-1,3 lipopolysaccharide (LPS) fucosyltransferase, as well as genes predicted to modulate diverse properties. In sum, our work suggests that data from consensus genome assemblies from single colonies may be misleading by failing to represent the variability present. Furthermore, we show that high-depth genomic sequencing data of a population can be analyzed to gain insight into the normal variation within bacterial strains.IMPORTANCE Although it is well known that many bacterial genomes are highly variable, it is nonetheless traditional to refer to, analyze, and publish "the genome" of a bacterial strain. Variability is usually reduced ("only sequence from a single colony"), ignored ("just publish the consensus"), or placed in the "too-hard" basket ("analysis of raw read data is more robust"). Now that whole-genome sequences are regularly used to assess virulence and track outbreaks, a better understanding of the baseline genomic variation present within single strains is needed. Here, we describe the variability seen in typical working stocks and colonies of pathogen Helicobacter pylori model strains SS1 and PMSS1 as revealed by use of high-coverage mate pair next-generation sequencing (NGS) and confirmed by traditional laboratory techniques. This work demonstrates that reliance on a consensus assembly as "the genome" of a bacterial strain may be misleading.
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Affiliation(s)
- Jenny L Draper
- Institute of Environmental Science and Research, Porirua, New Zealand
- Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, California, USA
- Department of Microbiology & Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA
| | - Lori M Hansen
- Departments of Medicine and Microbiology & Immunology, Center for Comparative Medicine, UC Davis, California, USA
| | - David L Bernick
- Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, California, USA
| | - Samar Abedrabbo
- Department of Microbiology & Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA
| | | | - Nguyet Kong
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, UC Davis, Davis, California, USA
| | - Bihua C Huang
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, UC Davis, Davis, California, USA
| | - Allison M Weis
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, UC Davis, Davis, California, USA
| | - Bart C Weimer
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, UC Davis, Davis, California, USA
| | - Arnoud H M van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Nader Pourmand
- Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, California, USA
| | - Jay V Solnick
- Departments of Medicine and Microbiology & Immunology, Center for Comparative Medicine, UC Davis, California, USA
| | - Kevin Karplus
- Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, California, USA
| | - Karen M Ottemann
- Department of Microbiology & Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA
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Sarkar P, Sumby P. Regulatory gene mutation: a driving force behind group a Streptococcus strain- and serotype-specific variation. Mol Microbiol 2016; 103:576-589. [PMID: 27868255 DOI: 10.1111/mmi.13584] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 01/13/2023]
Abstract
Data from multiple bacterial pathogens are consistent with regulator-encoding genes having higher mutation frequencies than the genome average. Such mutations drive both strain- and type- (e.g., serotype, haplotype) specific phenotypic heterogeneity, and may challenge public health due to the potential of variants to circumvent established treatment and/or preventative regimes. Here, using the human bacterial pathogen the group A Streptococcus (GAS; S. pyogenes) as a model organism, we review the types and regulatory-, phenotypic-, and disease-specific consequences of naturally occurring regulatory gene mutations. Strain-specific regulator mutations that will be discussed include examples that transform isolates into hyper-invasive forms by enhancing expression of immunomodulatory virulence factors, and examples that promote asymptomatic carriage of the organism. The discussion of serotype-specific regulator mutations focuses on serotype M3 GAS isolates, and how the identified rewiring of regulatory networks in this serotype may be contributing to a decades old epidemiological association of M3 isolates with particularly severe invasive infections. We conclude that mutation plays an outsized role in GAS pathogenesis and has clinical relevance. Given the phenotypic variability associated with regulatory gene mutations, the rapid examination of these genes in infecting isolates may inform with respect to potential patient complications and treatment options.
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Affiliation(s)
- Poulomee Sarkar
- Department of Microbiology & Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Paul Sumby
- Department of Microbiology & Immunology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
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Genomic Comparison of Campylobacter spp. and Their Potential for Zoonotic Transmission between Birds, Primates, and Livestock. Appl Environ Microbiol 2016; 82:7165-7175. [PMID: 27736787 DOI: 10.1128/aem.01746-16] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/30/2016] [Indexed: 12/30/2022] Open
Abstract
Campylobacter is the leading cause of human gastroenteritis worldwide. Wild birds, including American crows, are abundant in urban, suburban, and agricultural settings and are likely zoonotic vectors of Campylobacter Their proximity to humans and livestock increases the potential spreading of Campylobacter via crows between the environment, livestock, and humans. However, no studies have definitively demonstrated that crows are a vector for pathogenic Campylobacter We used genomics to evaluate the zoonotic and pathogenic potential of Campylobacter from crows to other animals with 184 isolates obtained from crows, chickens, cows, sheep, goats, humans, and nonhuman primates. Whole-genome analysis uncovered two distinct clades of Campylobacter jejuni genotypes; the first contained genotypes found only in crows, while a second genotype contained "generalist" genomes that were isolated from multiple host species, including isolates implicated in human disease, primate gastroenteritis, and livestock abortion. Two major β-lactamase genes were observed frequently in these genomes (oxa-184, 55%, and oxa-61, 29%), where oxa-184 was associated only with crows and oxa-61 was associated with generalists. Mutations in gyrA, indicative of fluoroquinolone resistance, were observed in 14% of the isolates. Tetracycline resistance (tetO) was present in 22% of the isolates, yet it occurred in 91% of the abortion isolates. Virulence genes were distributed throughout the genomes; however, cdtC alleles recapitulated the crow-only and generalist clades. A specific cdtC allele was associated with abortion in livestock and was concomitant with tetO These findings indicate that crows harboring a generalist C. jejuni genotype may act as a vector for the zoonotic transmission of Campylobacter IMPORTANCE: This study examined the link between public health and the genomic variation of Campylobacter in relation to disease in humans, primates, and livestock. Use of large-scale whole-genome sequencing enabled population-level assessment to find new genes that are linked to livestock disease. With 184 Campylobacter genomes, we assessed virulence traits, antibiotic resistance susceptibility, and the potential for zoonotic transfer to observe that there is a "generalist" genotype that may move between host species.
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Banerjee T, Sulthana S, Shelby T, Heckert B, Jewell J, Woody K, Karimnia V, McAfee J, Santra S. Multiparametric Magneto-fluorescent Nanosensors for the Ultrasensitive Detection of Escherichia coli O157:H7. ACS Infect Dis 2016; 2:667-673. [PMID: 27737552 DOI: 10.1021/acsinfecdis.6b00108] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Enterohemorrhagic Escherichia coli O157:H7 presents a serious threat to human health and sanitation and is a leading cause in many food- and waterborne ailments. While conventional bacterial detection methods such as PCR, fluorescent immunoassays and ELISA exhibit high sensitivity and specificity, they are relatively laborious and require sophisticated instruments. In addition, these methods often demand extensive sample preparation and have lengthy readout times. We propose a simpler and more sensitive diagnostic technique featuring multiparametric magneto-fluorescent nanosensors (MFnS). Through a combination of magnetic relaxation and fluorescence measurements, our nanosensors are able to detect bacterial contamination with concentrations as little as 1 colony-forming unit (CFU). The magnetic relaxation property of our MFnS allow for sensitive screening at low target CFU, which is complemented by fluorescence measurements of higher CFU samples. Together, these qualities allow for the detection and quantification of broad-spectrum contaminations in samples ranging from aquatic reservoirs to commercially produced food.
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Affiliation(s)
- Tuhina Banerjee
- Department of Chemistry, Kansas Polymer Research Center, Pittsburg State University, 1701 South Broadway Street, Pittsburg, Kansas 66762, United States
| | - Shoukath Sulthana
- Department of Chemistry, Kansas Polymer Research Center, Pittsburg State University, 1701 South Broadway Street, Pittsburg, Kansas 66762, United States
| | - Tyler Shelby
- Department of Chemistry, Kansas Polymer Research Center, Pittsburg State University, 1701 South Broadway Street, Pittsburg, Kansas 66762, United States
| | - Blaze Heckert
- Department of Chemistry, Kansas Polymer Research Center, Pittsburg State University, 1701 South Broadway Street, Pittsburg, Kansas 66762, United States
| | - Jessica Jewell
- Department of Chemistry, Kansas Polymer Research Center, Pittsburg State University, 1701 South Broadway Street, Pittsburg, Kansas 66762, United States
| | - Kalee Woody
- Department of Chemistry, Kansas Polymer Research Center, Pittsburg State University, 1701 South Broadway Street, Pittsburg, Kansas 66762, United States
| | - Vida Karimnia
- Department of Chemistry, Kansas Polymer Research Center, Pittsburg State University, 1701 South Broadway Street, Pittsburg, Kansas 66762, United States
| | - James McAfee
- Department of Chemistry, Kansas Polymer Research Center, Pittsburg State University, 1701 South Broadway Street, Pittsburg, Kansas 66762, United States
| | - Santimukul Santra
- Department of Chemistry, Kansas Polymer Research Center, Pittsburg State University, 1701 South Broadway Street, Pittsburg, Kansas 66762, United States
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Rubinelli P, Roto S, Kim SA, Park SH, Pavlidis HO, McIntyre D, Ricke SC. Reduction of Salmonella Typhimurium by Fermentation Metabolites of Diamond V Original XPC in an In Vitro Anaerobic Mixed Chicken Cecal Culture. Front Vet Sci 2016; 3:83. [PMID: 27695699 PMCID: PMC5025443 DOI: 10.3389/fvets.2016.00083] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/02/2016] [Indexed: 12/02/2022] Open
Abstract
Fermentation metabolites of Diamond V Original XPC™ (XPC), a biological product derived from yeast fermentation, were evaluated for their ability to reduce the Salmonella Typhimurium population using an in vitro mixed anaerobic culture system containing cecal microbiota to simulate chicken hindgut conditions. Four different samples were prepared: anaerobic mixed culture containing (1) feed only, (2) cecal only (ceca were harvested from 42 days old broiler chickens), (3) feed and cecal contents, and (4) feed, cecal contents, and 1% XPC. Two experimental conditions were investigated: Group 1, in which the cecal content was added at the same time as a S. Typhimurium marker strain and Group 2, in which the cecal content was preincubated for 24 h prior to the inoculation with the S. Typhimurium marker strain. The mixed cultures were incubated anaerobically at 37°C, and the S. Typhimurium marker strain was enumerated at 0, 24, and 48 h. Analysis of short chain fatty acids was also conducted for 24 h. In the Group 1 experiment, adding XPC did not exhibit significant reduction of S. Typhimurium. However, the presence of XPC resulted in rapid reduction of S. Typhimurium in Group 2. S. Typhimurium was reduced from 6.81 log10 CFU/ml (0 h) to 3.73 log10 CFU/ml and 1.19 log10 CFU/ml after 24 and 48 h, respectively. These levels were also 2.47 log10 and 2.72 log10 lower than the S. Typhimurium level recovered from the control culture with feed and cecal contents, but without XPC. Based on these results, it appears that the ability of XPC to reduce S. Typhimurium requires the presence of the cecal microbiota. Short chain fatty acid analysis indicated that acetate and butyrate concentrations of cultures containing XPC were twofold greater than the control cultures by 24 h of anaerobic growth. Results from the present study suggest that dietary inclusion of XPC may influence cecal microbiota fermentation and has the potential to reduce Salmonella in the cecum. Implications of these findings suggest that XPC may decrease preharvest levels of Salmonella in broilers and layers.
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Affiliation(s)
- Peter Rubinelli
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Stephanie Roto
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Sun Ae Kim
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Si Hong Park
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | | | | | - Steven C. Ricke
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
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Influence of Host Ecology and Behavior on Campylobacter jejuni Prevalence and Environmental Contamination Risk in a Synanthropic Wild Bird Species. Appl Environ Microbiol 2016; 82:4811-20. [PMID: 27260356 DOI: 10.1128/aem.01456-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 05/15/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Campylobacter jejuni is a foodborne pathogen that often leads to human infections through the consumption of contaminated poultry. Wild birds may play a role in the transmission of C. jejuni by acting as reservoir hosts. Despite ample evidence that wild birds harbor C. jejuni, few studies have addressed the role of host ecology in transmission to domestic animals or humans. We tested the hypothesis that host social behavior and habitat play a major role in driving transmission risk. C. jejuni infection and host ecology were studied simultaneously in wild American crows (Corvus brachyrhynchos) in Davis, CA, over 3 years. We found that 178 of 337 samples tested were culture positive (53%), with infection varying by season and host age. Among adult crows, infection rates were highest during the winter, when migrants return and crows form large communal roosts. Nestlings had the highest risk of infection, and whole-genome sequencing supports the observation of direct transmission between nestlings. We deployed global positioning system (GPS) receivers to quantify habitat use by crows; space use was nonrandom, with crows preferentially occupying some habitats while avoiding others. This behavior drastically amplified the risk of environmental contamination from feces in specific locations. This study demonstrates that social behavior contributes to infection within species and that habitat use leads to a heterogeneous risk of cross-species transmission. IMPORTANCE Campylobacter jejuni is the most common cause of gastroenteritis in industrialized countries. Despite efforts to reduce the colonization of poultry flocks and eventual infection of humans, the incidence of human C. jejuni infection has remained high. Because wild birds can harbor strains of C. jejuni that eventually infect humans, there has long been speculation that wild birds might act as an important reservoir in the C. jejuni infection cycle. We simultaneously studied infection prevalence, social behavior, and movement ecology in wild American crows (Corvus brachyrhynchos). We found that social behavior contributed to patterns of infection and that movement behavior resulted in some areas having a high risk of transmission while others had a low risk. The incorporation of ecological data into studies of C. jejuni in wild birds has the potential to resolve when and how wild birds contribute to domestic animal and human C. jejuni infection, leading to better control of initial poultry contamination.
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Zhang H, Susanto TT, Wan Y, Chen SL. Comprehensive mutagenesis of the fimS promoter regulatory switch reveals novel regulation of type 1 pili in uropathogenic Escherichia coli. Proc Natl Acad Sci U S A 2016; 113:4182-7. [PMID: 27035967 PMCID: PMC4839427 DOI: 10.1073/pnas.1522958113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Type 1 pili (T1P) are major virulence factors for uropathogenic Escherichia coli (UPEC), which cause both acute and recurrent urinary tract infections. T1P expression therefore is of direct relevance for disease. T1P are phase variable (both piliated and nonpiliated bacteria exist in a clonal population) and are controlled by an invertible DNA switch (fimS), which contains the promoter for the fim operon encoding T1P. Inversion of fimS is stochastic but may be biased by environmental conditions and other signals that ultimately converge at fimS itself. Previous studies of fimS sequences important for T1P phase variation have focused on laboratory-adapted E coli strains and have been limited in the number of mutations or by alteration of the fimS genomic context. We surmounted these limitations by using saturating genomic mutagenesis of fimS coupled with accurate sequencing to detect both mutations and phase status simultaneously. In addition to the sequences known to be important for biasing fimS inversion, our method also identifies a previously unknown pair of 5' UTR inverted repeats that act by altering the relative fimA levels to control phase variation. Thus we have uncovered an additional layer of T1P regulation potentially impacting virulence and the coordinate expression of multiple pilus systems.
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Affiliation(s)
- Huibin Zhang
- Infectious Diseases Group, Genome Institute of Singapore, Singapore 138672
| | - Teodorus T Susanto
- Stem Cell and Development, Genome Institute of Singapore, Singapore 138672
| | - Yue Wan
- Stem Cell and Development, Genome Institute of Singapore, Singapore 138672
| | - Swaine L Chen
- Infectious Diseases Group, Genome Institute of Singapore, Singapore 138672; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074
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Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Suffredini AF, Sacks DB, Yu YK. Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:194-210. [PMID: 26510657 PMCID: PMC4723618 DOI: 10.1007/s13361-015-1271-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/04/2015] [Accepted: 09/05/2015] [Indexed: 05/13/2023]
Abstract
Correct and rapid identification of microorganisms is the key to the success of many important applications in health and safety, including, but not limited to, infection treatment, food safety, and biodefense. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is challenging correct microbial identification because of the large number of choices present. To properly disentangle candidate microbes, one needs to go beyond apparent morphology or simple 'fingerprinting'; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptidome profiles of microbes to better separate them and by designing an analysis method that yields accurate statistical significance. Here, we present an analysis pipeline that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using MS/MS data of 81 samples, each composed of a single known microorganism, that the proposed pipeline can correctly identify microorganisms at least at the genus and species levels. We have also shown that the proposed pipeline computes accurate statistical significances, i.e., E-values for identified peptides and unified E-values for identified microorganisms. The proposed analysis pipeline has been implemented in MiCId, a freely available software for Microorganism Classification and Identification. MiCId is available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html . Graphical Abstract ᅟ.
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Affiliation(s)
- Gelio Alves
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Guanghui Wang
- Proteomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Steven K Drake
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marjan Gucek
- Proteomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anthony F Suffredini
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David B Sacks
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yi-Kuo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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Miller EW, Danger JL, Ramalinga AB, Horstmann N, Shelburne SA, Sumby P. Regulatory rewiring confers serotype-specific hyper-virulence in the human pathogen group A Streptococcus. Mol Microbiol 2015; 98:473-89. [PMID: 26192205 DOI: 10.1111/mmi.13136] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2015] [Indexed: 12/18/2022]
Abstract
Phenotypic heterogeneity is commonly observed between isolates of a given pathogen. Epidemiological analyses have identified that some serotypes of the group A Streptococcus (GAS) are non-randomly associated with particular disease manifestations. Here, we present evidence that a contributing factor to the association of serotype M3 GAS isolates with severe invasive infections is the presence of a null mutant allele for the orphan kinase RocA. Through use of RNAseq analysis, we identified that the natural rocA mutation present within M3 isolates leads to the enhanced expression of more than a dozen immunomodulatory virulence factors, enhancing phenotypes such as hemolysis and NAD(+) hydrolysis. Consequently, an M3 GAS isolate survived human phagocytic killing at a level 13-fold higher than a rocA complemented derivative, and was significantly more virulent in a murine bacteremia model of infection. Finally, we identified that RocA functions through the CovR/S two-component system as levels of phosphorylated CovR increase in the presence of functional RocA, and RocA has no regulatory activity following covR or covS mutation. Our data are consistent with RocA interfacing with the CovR/S two-component system, and that the absence of this activity in M3 GAS potentiates the severity of invasive infections caused by isolates of this serotype.
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Affiliation(s)
- Eric W Miller
- Department of Microbiology & Immunology, School of Medicine, University of Nevada, Reno, Nevada, USA
| | - Jessica L Danger
- Department of Microbiology & Immunology, School of Medicine, University of Nevada, Reno, Nevada, USA
| | - Anupama B Ramalinga
- Department of Microbiology & Immunology, School of Medicine, University of Nevada, Reno, Nevada, USA
| | - Nicola Horstmann
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, Texas, USA
| | - Samuel A Shelburne
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, Texas, USA
| | - Paul Sumby
- Department of Microbiology & Immunology, School of Medicine, University of Nevada, Reno, Nevada, USA
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Kubicek-Sutherland JZ, Heithoff DM, Ersoy SC, Shimp WR, House JK, Marth JD, Smith JW, Mahan MJ. Host-dependent Induction of Transient Antibiotic Resistance: A Prelude to Treatment Failure. EBioMedicine 2015; 2:1169-78. [PMID: 26501114 PMCID: PMC4588393 DOI: 10.1016/j.ebiom.2015.08.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/31/2015] [Accepted: 08/05/2015] [Indexed: 01/03/2023] Open
Abstract
Current antibiotic testing does not include the potential influence of host cell environment on microbial susceptibility and antibiotic resistance, hindering appropriate therapeutic intervention. We devised a strategy to identify the presence of host–pathogen interactions that alter antibiotic efficacy in vivo. Our findings revealed a bacterial mechanism that promotes antibiotic resistance in vivo at concentrations of drug that far exceed dosages determined by standardized antimicrobial testing. This mechanism has escaped prior detection because it is reversible and operates within a subset of host tissues and cells. Bacterial pathogens are thereby protected while their survival promotes the emergence of permanent drug resistance. This host-dependent mechanism of transient antibiotic resistance is applicable to multiple pathogens and has implications for the development of more effective antimicrobial therapies. Standard MIC testing does not consider the influence of the host milieu, potentially hindering therapeutic intervention. Salmonella induce polymyxin resistance during infection at levels of drug that far exceed dosages determined by MIC testing. Polymyxin treatment failed to control Salmonella infection and promotes the emergence of drug-resistant mutants.
Physicians rely on laboratory antimicrobial susceptibility testing of clinical isolates to identify a suitable antibiotic for therapy. Although the recommended antibiotics clear most bacterial infections, some patients fail to respond and require prolonged therapy, higher dosing or different antibiotics. Why does this occur and what are the possible implications? By studying antibiotic resistance in the context of infection, we identified a host-dependent mechanism that promotes antibiotic resistance at concentrations of drug that far exceed dosages determined by standardized antimicrobial testing. These findings question current antibiotic testing methods that have guided physician treatment practices and drug development for the last several decades.
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Affiliation(s)
| | - Douglas M Heithoff
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA ; Center for Nanomedicine, University of California, Santa Barbara, CA 93106, USA
| | - Selvi C Ersoy
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - William R Shimp
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - John K House
- University of Sydney, Faculty of Veterinary Science, Camden, NSW, Australia
| | - Jamey D Marth
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA ; Center for Nanomedicine, University of California, Santa Barbara, CA 93106, USA ; Sanford-Burnham Medical Research Institute, Cancer Research Center, La Jolla, CA 92037, USA
| | - Jeffrey W Smith
- Sanford-Burnham Medical Research Institute, Cancer Research Center, La Jolla, CA 92037, USA
| | - Michael J Mahan
- Dept. of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA ; Center for Nanomedicine, University of California, Santa Barbara, CA 93106, USA
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Deng X, Desai PT, den Bakker HC, Mikoleit M, Tolar B, Trees E, Hendriksen RS, Frye JG, Porwollik S, Weimer BC, Wiedmann M, Weinstock GM, Fields PI, McClelland M. Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages. Emerg Infect Dis 2015; 20:1481-9. [PMID: 25147968 PMCID: PMC4178404 DOI: 10.3201/eid2009.131095] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Major lineages emerged during the 17th–18th centuries and diversified during the 1920s and 1950s. Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains from 2 different sequencing platforms. Five major genetic lineages were recognized, which revealed possible patterns of geographic and epidemiologic distribution. Analyses on the population dynamics and evolutionary history estimated that major lineages emerged during the 17th–18th centuries and diversified during the 1920s and 1950s.
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Römling U. Small molecules with big effects: Cyclic di-GMP-mediated stimulation of cellulose production by the amino acid ʟ-arginine. Sci Signal 2015; 8:fs12. [PMID: 26060328 DOI: 10.1126/scisignal.aac4734] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this issue of Science Signaling, Mills et al. show that the amino acid ʟ-arginine increases the concentration of the second messenger c-di-GMP in Salmonella enterica serovar Typhimurium through a specific diguanylate cyclase, leading to increased production of the exopolysaccharide cellulose, which is an extracellular matrix component of environmental and host-associated biofilms.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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43
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Development of a Salmonella cross-protective vaccine for food animal production systems. Vaccine 2015; 33:100-7. [DOI: 10.1016/j.vaccine.2014.11.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/07/2014] [Accepted: 11/08/2014] [Indexed: 11/20/2022]
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Baquero F, Lanza VF, Cantón R, Coque TM. Public health evolutionary biology of antimicrobial resistance: priorities for intervention. Evol Appl 2014; 8:223-39. [PMID: 25861381 PMCID: PMC4380917 DOI: 10.1111/eva.12235] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/12/2014] [Indexed: 12/19/2022] Open
Abstract
The three main processes shaping the evolutionary ecology of antibiotic resistance (AbR) involve the emergence, invasion and occupation by antibiotic-resistant genes of significant environments for human health. The process of emergence in complex bacterial populations is a high-frequency, continuous swarming of ephemeral combinatory genetic and epigenetic explorations inside cells and among cells, populations and communities, expanding in different environments (migration), creating the stochastic variation required for evolutionary progress. Invasion refers to the process by which AbR significantly increases in frequency in a given (invaded) environment, led by external invaders local multiplication and spread, or by endogenous conversion. Conversion occurs because of the spread of AbR genes from an exogenous resistant clone into an established (endogenous) bacterial clone(s) colonizing the environment; and/or because of dissemination of particular resistant genetic variants that emerged within an endogenous clonal population. Occupation of a given environment by a resistant variant means a permanent establishment of this organism in this environment, even in the absence of antibiotic selection. Specific interventions on emergence influence invasion, those acting on invasion also influence occupation and interventions on occupation determine emergence. Such interventions should be simultaneously applied, as they are not simple solutions to the complex problem of AbR.
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Affiliation(s)
- Fernando Baquero
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Madrid, Spain ; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain ; CIBER Epidemiología y Salud Pública (CIBERESP) Madrid, Spain
| | - Val F Lanza
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Madrid, Spain ; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain ; CIBER Epidemiología y Salud Pública (CIBERESP) Madrid, Spain
| | - Rafael Cantón
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Madrid, Spain ; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain ; Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III Madrid, Spain
| | - Teresa M Coque
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Madrid, Spain ; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC) Madrid, Spain ; CIBER Epidemiología y Salud Pública (CIBERESP) Madrid, Spain
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Zacarías M, Reinheimer J, Forzani L, Grangette C, Vinderola G. Mortality and translocation assay to study the protective capacity of Bifidobacterium lactis INL1 against Salmonella Typhimurium infection in mice. Benef Microbes 2014; 5:427-36. [DOI: 10.3920/bm2013.0086] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mouse has been largely used for the study of the protective capacity of probiotics against intestinal infections caused by Salmonella. In this work we aimed at comparing the mortality and translocation assay for the study of the protective capacity of the human breast milk-derived strain Bifidobacterium animalis subsp. lactis INL1 on a model of gut infection by Salmonella enterica subsp. enterica serovar Typhimurium. Different doses of S. Typhimurium FUNED and B. animalis subsp. lactis INL 1 were administered to Balb/c mice in a mortality or a translocation assay. The survival of the control group in the mortality assay resulted to be variable along experiments, and then we preferred to use a translocation assay where the preventive administration of 109 cfu of bifidobacteria/mouse for 10 consecutive days significantly reduced the number of infected animals and the levels of translocation to liver and spleen, with enhanced secretory immunoglobulin A and interleukin 10 production in the small and large intestine, respectively. Ten days of B. animalis subsp. lactis strain INL1 administration to mice significantly reduced both the incidence and the severity of Salmonella infection in a mouse model of translocation. This work provided the first evidence that a translocation assay, compared to a mortality assay, could be more useful to study the protective capacity of probiotics against Salmonella infection, as more information can be obtained from mice and less suffering is conferred to animals due to the fact that the mortality assay is shorter than the latter. These facts are in line with the guidelines of animal research recently established by the National Centre for the Replacement, Refinement & Reduction of Animals in Research.
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Affiliation(s)
- M.F. Zacarías
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santiago del Estero 2829, Santa Fe (3000), Argentina
| | - J. Reinheimer
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santiago del Estero 2829, Santa Fe (3000), Argentina
| | - L. Forzani
- Departamento de Matemática, Facultad de Ingeniería Química, Universidad Nacional del Litoral and Instituto de Matemática Aplicada del Litoral (CONICET-UNL), Santa Fe (3000), Argentina
| | - C. Grangette
- Lactic Acid Bacteria and Mucosal Immunity, Center for Infection and Immunity of Lille, Pasteur Institute of Lille, INSERM U1019 - CNRS UMR 8204, Lille, France
| | - G. Vinderola
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santiago del Estero 2829, Santa Fe (3000), Argentina
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Mahan MJ, Heithoff DM, House JK. Salmonella cross-protective vaccines: fast-forward to the next generation of food safety. Future Microbiol 2014; 7:805-8. [PMID: 22827301 DOI: 10.2217/fmb.12.60] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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47
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Shariat N, Dudley EG. Where are we heading with Salmonella molecular subtyping? Future Microbiol 2014; 8:1231-3. [PMID: 24059912 DOI: 10.2217/fmb.13.107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Nikki Shariat
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
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Abstract
Different species inhabit different sensory worlds and thus have evolved diverse means of processing information, learning and memory. In the escalated arms race with host defense, each pathogenic bacterium not only has evolved its individual cellular sensing and behavior, but also collective sensing, interbacterial communication, distributed information processing, joint decision making, dissociative behavior, and the phenotypic and genotypic heterogeneity necessary for epidemiologic success. Moreover, pathogenic populations take advantage of dormancy strategies and rapid evolutionary speed, which allow them to save co-generated intelligent traits in a collective genomic memory. This review discusses how these mechanisms add further levels of complexity to bacterial pathogenicity and transmission, and how mining for these mechanisms could help to develop new anti-infective strategies.
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Affiliation(s)
- Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig Braunschweig, Germany
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49
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Kubicek-Sutherland JZ, Heithoff DM, Ersoy SC, Shimp WR, Mahan MJ. Immunization with a DNA adenine methylase over-producing Yersinia pseudotuberculosis vaccine confers robust cross-protection against heterologous pathogenic serotypes. Vaccine 2014; 32:1451-9. [PMID: 24508035 DOI: 10.1016/j.vaccine.2014.01.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/04/2014] [Accepted: 01/14/2014] [Indexed: 01/09/2023]
Abstract
Yersinia pseudotuberculosis is a foodborne pathogen that can cause serious human illness. Although the source and route of transmission often remain obscure, livestock have been implicated in some cases. The diversity of yersiniae present on farms and their widespread distribution in animal and environmental reservoirs necessitates the use of broad prophylactic strategies that are efficacious against many serotypes simultaneously. Herein, immunization of mice with a modified, live attenuated Y. pseudotuberculosis vaccine that overproduces the DNA adenine methylase (Dam(OP)) conferred robust protection against virulent challenge (150-fold LD50) with homologous and heterologous serotypes that have been associated with human disease (O:1, O:1a, O:3). Further, the dam gene was shown to be essential for cell viability in all (7 of 7) Y. pseudotuberculosis strains tested. Direct selection for the inheritance of dam mutant alleles in Y. pseudotuberculosis resulted in dam strain variants that contained compensatory (second-site suppressor) mutations in genes encoding methyl-directed mismatch repair proteins (mutHLS) that are involved in suppression of the non-viable cell phenotype in all (19/19) strains tested. Such dam mutH variants exhibited a significant increase in virulence and spontaneous mutation frequency relative to that of a Dam(OP) vaccine strain. These studies indicate that Y. pseudotuberculosis Dam(OP) strains conferred potent cross-protective efficacy as well as decreased virulence and spontaneous mutation frequency relative to those that lack Dam, which have compensatory mutations in mutHLS loci. These data suggest that development of yersiniae livestock vaccines based on Dam overproduction is a viable mitigation strategy to reduce these potential foodborne contaminants.
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Affiliation(s)
- Jessica Z Kubicek-Sutherland
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Douglas M Heithoff
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Selvi C Ersoy
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - William R Shimp
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
| | - Michael J Mahan
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
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Haemophilus responses to nutritional immunity: epigenetic and morphological contribution to biofilm architecture, invasion, persistence and disease severity. PLoS Pathog 2013; 9:e1003709. [PMID: 24130500 PMCID: PMC3795038 DOI: 10.1371/journal.ppat.1003709] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 08/30/2013] [Indexed: 12/18/2022] Open
Abstract
In an effort to suppress microbial outgrowth, the host sequesters essential nutrients in a process termed nutritional immunity. However, inflammatory responses to bacterial insult can restore nutritional resources. Given that nutrient availability modulates virulence factor production and biofilm formation by other bacterial species, we hypothesized that fluctuations in heme-iron availability, particularly at privileged sites, would similarly influence Haemophilus biofilm formation and pathogenesis. Thus, we cultured Haemophilus through sequential heme-iron deplete and heme-iron replete media to determine the effect of transient depletion of internal stores of heme-iron on multiple pathogenic phenotypes. We observed that prior heme-iron restriction potentiates biofilm changes for at least 72 hours that include increased peak height and architectural complexity as compared to biofilms initiated from heme-iron replete bacteria, suggesting a mechanism for epigenetic responses that participate in the changes observed. Additionally, in a co-infection model for human otitis media, heme-iron restricted Haemophilus, although accounting for only 10% of the inoculum (90% heme-iron replete), represented up to 99% of the organisms recovered at 4 days. These data indicate that fluctuations in heme-iron availability promote a survival advantage during disease. Filamentation mediated by a SulA-related ortholog was required for optimal biofilm peak height and persistence during experimental otitis media. Moreover, severity of disease in response to heme-iron restricted Haemophilus was reduced as evidenced by lack of mucosal destruction, decreased erythema, hemorrhagic foci and vasodilatation. Transient restriction of heme-iron also promoted productive invasion events leading to the development of intracellular bacterial communities. Taken together, these data suggest that nutritional immunity, may, in fact, foster long-term phenotypic changes that better equip bacteria for survival at infectious sites. Clinical management of upper and lower respiratory tract diseases caused by nontypeable Haemophilus influenzae (NTHI) is a significant socioeconomic burden. Therapies targeting the pathogenic lifestyle of NTHI remain non-existent due to a lack of understanding of host microenvironmental cues and bacterial responses that dictate NTHI persistence. Iron availability influences bacterial virulence traits and biofilm formation; yet, host sequestration of iron serves to restrict bacterial growth. We predicted that fluctuations in availability of iron-containing compounds, typically associated with infection, would impact NTHI pathogenesis. We demonstrated that transient restriction of heme-iron triggered an epigenetic developmental program that enhanced NTHI biofilm architecture, directly influenced by induced morphological changes in bacterial length. Heme-iron restricted bacteria were primed for survival in the mammalian middle ear, due in part to an observed reduction in host inflammation coinciding with a striking reduction in host mucosal epithelial damage, compared to that observed in response to heme-iron replete NTHI. Moreover, transiently restricted NTHI were more invasive of epithelial cells resulting in formation of intracellular bacterial communities. Our findings significantly advance our understanding of how host immune pressure and nutrient availability influence pathogenic behaviors that impact disease severity.
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